Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016181.1 Corchorus capsularis cultivar CVL-1 contig16202, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 16444
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32


Found at i:11 original size:2 final size:2

Alignment explanation


    Indices: 5--38  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

          1 TCAA

                                                              
          5 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

         39 TTAGGCCATG


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:74 original size:11 final size:11

Alignment explanation


    Indices: 58--88  Score: 53
    Period size: 11  Copynumber: 2.8  Consensus size: 11

         48 GTCTCTGATT

                       
         58 TATACTATATA
          1 TATACTATATA

                       
         69 TATACTATATA
          1 TATACTATATA

                *    
         80 TATAATATA
          1 TATACTATA

         89 ATAGACTTTC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45


Consensus pattern (11 bp):   
TATACTATATA

Found at i:2840 original size:87 final size:87

Alignment explanation


    Indices: 2679--2993  Score: 378
    Period size: 87  Copynumber: 3.6  Consensus size: 87

       2669 TCATTTTGAA

                 *      *  *              *  *     **                        
       2679 CTGTTCGAAAATGTGTTGCACCGAGCTCACTGACTTCCTTTCTTTAAAGAAATGCACCGCCTTAA
          1 CTGTTTGAAAATATGCTGCACCGAGCTCACCGAATT-C-AACTTTAAAGAAATGCACCGCCTTAA

                           *        
       2744 CTTGATTCACCGAATCACCATGAT
         64 CTTGATTCACCGAATGACCATGAT

              *              *                         *              *    * 
       2768 CTATTTGAAAATATGCTACACCGAGCTCACCGAATTCAACTTTTAAGAAATGCACCGCATTAATT
          1 CTGTTTGAAAATATGCTGCACCGAGCTCACCGAATTCAACTTTAAAGAAATGCACCGCCTTAACT

                                  
       2833 TGATTCACCGAATGACCATGAT
         66 TGATTCACCGAATGACCATGAT

                                                       *                  ** 
       2855 CTGTTTGAAAATATGCTGCACCGAGCTCACCGAATTCAACTTTGAAGAAATAAGGCACCGCCCCA
          1 CTGTTTGAAAATATGCTGCACCGAGCTCACCGAATTCAACTTTAAAGAAAT---GCACCGCCTTA

                              * *   *
       2920 ACTTGATTCACCGAATGATCTTGAA
         63 ACTTGATTCACCGAATGACCATGAT

                        *     *                *             
       2945 CTGTTTGAAAATCTGCTGTACCGAGCTCACCGAATCCAATCTTTAAAGA
          1 CTGTTTGAAAATATGCTGCACCGAGCTCACCGAATTCAA-CTTTAAAGA

       2994 TGTTACACCG


Statistics
Matches: 195,  Mismatches: 27, Indels: 6
        0.86            0.12        0.03

Matches are distributed among these distances:
  87   92  0.47
  88    1  0.01
  89   29  0.15
  90   65  0.33
  91    8  0.04

ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28


Consensus pattern (87 bp):   
CTGTTTGAAAATATGCTGCACCGAGCTCACCGAATTCAACTTTAAAGAAATGCACCGCCTTAACT
TGATTCACCGAATGACCATGAT

Found at i:7508 original size:2 final size:2

Alignment explanation


    Indices: 7453--7489  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       7443 GTGCAACAAA

                                                                   
       7453 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       7490 CACCAAGGAA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:11353 original size:21 final size:21

Alignment explanation


    Indices: 11329--11369  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      11319 CATCTGAGTA

                       *         
      11329 TTCGCAGCTTCCTCTCGGCGC
          1 TTCGCAGCTTCATCTCGGCGC

                 **             
      11350 TTCGCCTCTTCATCTCGGCG
          1 TTCGCAGCTTCATCTCGGCG

      11370 TGCTAACTCT


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.05, C:0.41, G:0.22, T:0.32


Consensus pattern (21 bp):   
TTCGCAGCTTCATCTCGGCGC
Done.